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- Bernal, Ximena E., et al.
(författare)
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Empowering Latina scientists
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 363:6429, s. 825-826
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 5. |
- Emami Khoonsari, Payam, et al.
(författare)
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Interoperable and scalable data analysis with microservices : Applications in metabolomics
- 2019
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 35:19, s. 3752-3760
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Tidskriftsartikel (refereegranskat)abstract
- MotivationDeveloping a robust and performant data analysis workflow that integrates all necessary components whilst still being able to scale over multiple compute nodes is a challenging task. We introduce a generic method based on the microservice architecture, where software tools are encapsulated as Docker containers that can be connected into scientific workflows and executed using the Kubernetes container orchestrator.ResultsWe developed a Virtual Research Environment (VRE) which facilitates rapid integration of new tools and developing scalable and interoperable workflows for performing metabolomics data analysis. The environment can be launched on-demand on cloud resources and desktop computers. IT-expertise requirements on the user side are kept to a minimum, and workflows can be re-used effortlessly by any novice user. We validate our method in the field of metabolomics on two mass spectrometry, one nuclear magnetic resonance spectroscopy and one fluxomics study. We showed that the method scales dynamically with increasing availability of computational resources. We demonstrated that the method facilitates interoperability using integration of the major software suites resulting in a turn-key workflow encompassing all steps for mass-spectrometry-based metabolomics including preprocessing, statistics and identification. Microservices is a generic methodology that can serve any scientific discipline and opens up for new types of large-scale integrative science.
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- Gutiérrez, Alicia, et al.
(författare)
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Replenishment and mobilization of intracellular nitrogen pools decouples wine yeast nitrogen uptake from growth.
- 2016
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Ingår i: Applied microbiology and biotechnology. - : Springer Science and Business Media LLC. - 1432-0614 .- 0175-7598. ; 100:7, s. 3255-65
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Tidskriftsartikel (refereegranskat)abstract
- Wine yeast capacity to take up nitrogen from the environment and catabolize it to support population growth, fermentation, and aroma production is critical to wine production. Under nitrogen restriction, yeast nitrogen uptake is believed to be intimately coupled to reproduction with nitrogen catabolite repression (NCR) suggested mediating this link. We provide a time- and strain-resolved view of nitrogen uptake, population growth, and NCR activity in wine yeasts. Nitrogen uptake was found to be decoupled from growth due to early assimilated nitrogen being used to replenish intracellular nitrogen pools rather than being channeled directly into reproduction. Internally accumulated nitrogen was later mobilized to support substantial population expansion after external nitrogen was depleted. On good nitrogen sources, the decoupling between nitrogen uptake and growth correlated well with relaxation of NCR repression, raising the potential that the latter may be triggered by intracellular build-up of nitrogen. No link between NCR activity and nitrogen assimilation or growth on poor nitrogen sources was found. The decoupling between nitrogen uptake and growth and its influence on NCR activity is of relevance for both wine production and our general understanding of nitrogen use.
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| 7. |
- Lappalainen, Tuuli, et al.
(författare)
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Transcriptome and genome sequencing uncovers functional variation in humans
- 2013
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 501:7468, s. 506-511
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Tidskriftsartikel (refereegranskat)abstract
- Genome sequencing projects are discovering millions of genetic variants in humans, and interpretation of their functional effects is essential for understanding the genetic basis of variation in human traits. Here we report sequencing and deep analysis of messenger RNA and microRNA from lymphoblastoid cell lines of 462 individuals from the 1000 Genomes Project-the first uniformly processed high-throughput RNA-sequencing data from multiple human populations with high-quality genome sequences. We discover extremely widespread genetic variation affecting the regulation of most genes, with transcript structure and expression level variation being equally common but genetically largely independent. Our characterization of causal regulatory variation sheds light on the cellular mechanisms of regulatory and loss-of-function variation, and allows us to infer putative causal variants for dozens of disease-associated loci. Altogether, this study provides a deep understanding of the cellular mechanisms of transcriptome variation and of the landscape of functional variants in the human genome.
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| 8. |
- Lebedev, Alexander, et al.
(författare)
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Feasibility study and experimental verification of simplified fiber-supported 60-GHz picocell mobile backhaul links
- 2013
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Ingår i: IEEE Photonics Journal. - : Institute of Electrical and Electronics Engineers (IEEE). - 1943-0655. ; 5:4, s. 7200913-7200913
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Tidskriftsartikel (refereegranskat)abstract
- We propose and experimentally demonstrate a fiber-wireless transmission system for optimized delivery of 60-GHz radio frequency (RF) signals through picocell mobile backhaul connections. We identify advantages of 60-GHz links for utilization in short-range mobile backhaul through feasibility analysis and comparison with an alternative E-band (60-90 GHz) technology. The 60-GHz fiber-wireless-fiber setup is then introduced: two spans of up to 20 km of optical fiber are deployed and bridged by up to 4 m of wireless distance. The 60-GHz radio-over-fiber technology is utilized in the first span of fiber transmission. The system is simplified and tailored for delivery of on-off keying data signals by employing a single module for lightwave generation and modulation combined with a simplified RF downconversion technique by envelope detection. Data signals of 1.25 Gb/s are transmitted, and a bit-error-rate performance below the 7% overhead forward-error-correction limit is achieved for a range of potential fiber deployment scenarios. A spurious free dynamic range of 73 dB-Hz2/3 is attained for a frequency-doubling photonic RF upconversion technique. The power budget margin that is required to extend the wireless transmission distance from 4 m to a few hundred meters has been taken into account in the setup design, and the techniques to extend the wireless distance are analyzed.
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- Pang, Xiaodan, 1986-, et al.
(författare)
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Centralized optical-frequency-comb-based RF carrier generator for DWDM fiber-wireless access systems
- 2014
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Ingår i: Journal of Optical Communications and Networking. - : Optical Society of America. - 1943-0620 .- 1943-0639. ; 6:1, s. 1-7
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we report on a gigabit capacity fiber-wireless system that enables smooth integration between high-speed wireless networks and dense wavelength-division-multiplexing (DWDM) access networks. By employing a centralized optical frequency comb, both the wireline and the wireless services for each DWDM user can be simultaneously supported. Besides, each baseband channel can be transparently upconverted to multiple radio-frequency (RF) bands for different wireless standards, which can be flexibly filtered at the end user to select the on-demand RF band, depending on the wireless applications. For demonstration, we transmit a 2.5 Gbit/s signal through the proposed system and successfully achieve a bit-error-rate (BER) performance well below the 7% overhead forward error correction limit of the BER of 2 x 10(-3) for both the wireline and the wireless signals in the 60 GHz band after 25 km single-mode fiber plus up to 6 m wireless distance.
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